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 *  * If the subject names under your !FreeSurfer SUBJECTS_DIR directory do not match the subject/session names that they have in the BIDS structure, then you have to edit the configuration file to make sure that the '''subjlist''' variable contains the names they have in your SUBJECTS_DIR (i.e., the names that you used when you ran [[recon-all]] on the structural images).
 * If this is a longitudinal study, then the '''subjlist''' and '''baselist''' variable in the configuration file must match, respectively, the time point and base names in your SUBJECTS_DIR (i.e., the names that you used when you ran the longitudinal stream of [[recon-all]] on the structural images).
 * If at least one of your subjects has DWIs from multiple sessions (this means multiple visits, not multiple DWI scans in the same visit), then we will assume that this is a longitudinal study and the configuration file will be set up to run the longitudinal stream of TRACULA. If this is not the case and, for example, the duplicate sessions should not be used in the analysis, then you have to edit the configuration file to remove all entries related to those sessions, and to remove the '''baselist''' variable.

Index

Name

dmri_bids_config: Configure TRACULA to run on a BIDS-formatted dataset

Usage

dmri_bids_config --in <directory> --c <configfile>

This script will take as its input a BIDS-formatted study directory and output:

  1. A TRACULA configuration file: This file is needed to pre-process the DWI data, reconstruct tracts of interest, etc. with trac-all.

  2. A FreeSurfer Group Descriptor (FSGD) file: This file is needed to perform statistics on the output tract measures with mri_glmfit. It will be generated if the input BIDS directory contains a participants.tsv file.

Arguments

Required arguments

  • --in <directory>

    Path to the input data (the top-level BIDS directory for the study, not a single subject or session directory)

At least one of the following two is required:

  • --c <file>

    Output configuration file that specifies DWI inputs and analysis options for TRACULA

    --f <file>

    Output FSGD file that specifies subject-specific continuous and discrete variables for linear regression analyses (default: append .fsgd to the argument of --c)

Optional arguments

  • --fsdir <directory>

    FreeSurfer SUBJECTS_DIR for this study (must be specified, either here or with: setenv SUBJECTS_DIR ...)

    --trdir <directory>

    Output TRACULA directory for this study (If not specified, TRACULA will use the FreeSurfer SUBJECTS_DIR)

    --acq <name>

    Only use DWI scans collected with this acquisition (The name of the NIfTI volumes in BIDS must include the string acq- followed by this name)

After you run dmri_bids_config

It is important that you inspect the configuration file generated by this script to make sure that everything has been set up the way you intended. It is not always possible to guess the intentions of the investigator from the contents of BIDS directory structure. The TRACULA configuration file is a simple text file that you can edit as you wish before initiating data analysis.

A few examples of situations where you may have to edit the configuration file:

  • If the subject names under your FreeSurfer SUBJECTS_DIR directory do not match the subject/session names that they have in the BIDS structure, then you have to edit the configuration file to make sure that the subjlist variable contains the names they have in your SUBJECTS_DIR (i.e., the names that you used when you ran recon-all on the structural images).

  • If this is a longitudinal study, then the subjlist and baselist variable in the configuration file must match, respectively, the time point and base names in your SUBJECTS_DIR (i.e., the names that you used when you ran the longitudinal stream of recon-all on the structural images).

  • If at least one of your subjects has DWIs from multiple sessions (this means multiple visits, not multiple DWI scans in the same visit), then we will assume that this is a longitudinal study and the configuration file will be set up to run the longitudinal stream of TRACULA. If this is not the case and, for example, the duplicate sessions should not be used in the analysis, then you have to edit the configuration file to remove all entries related to those sessions, and to remove the baselist variable.

See also

dmrirc, trac-all

Links

TRACULA

References

If you use TRACULA, please cite:

If you use our measures of head motion, please cite:

If you use the longitudinal stream of TRACULA, please cite:

Reporting Bugs

Report bugs to < analysis-bugs@nmr.mgh.harvard.edu >

Author/s

Anastasia Yendiki

dmri_bids_config (last edited 2021-12-08 22:43:57 by AnastasiaYendiki)